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ARGGHH!
Do you have your template(s) and nothing but templates in the Templates folder? Do you have your site defined properly in DW's site management area? How exactly are you creating these links that don't work? What is DW putting in there for the links?
Please provide an example of the link that DW creates. What do you have to change that to? And what specifically doesn't work? When you "preview in browser" do you have DW set to use a temp file? Do the links work when you upload the files to your server?